Human pluripotent stem cell-derived kidney organoids reveal tubular epithelial pathobiology of heterozygous HNF1B-associated dysplastic kidney malformations

• DOI: 10.1016/j.stemcr.2024.04.011
• Publication Date: 2024-05-23T14:35:21Z
• Authors: Ioannis Bantounas; Kirsty M. Rooney; Filipa M. Lopes; Faris Tengku; Steven Woods; Leo A.H. Zeef; I-Hsuan Lin; Shweta Y. Kuba; Nicola Bates; Sandra Hummelgaard; Katherine A. Hillman; Silvia Cereghini; Adrian S. Woolf; Susan J. Kimber
• Keywords: Pluripotent Stem Cells; HNF1B; Heterozygote; kidney disease; organoid; Induced Pluripotent Stem Cells; Kidney; Article; 03 medical and health sciences; cAMP; proximal tubule; Humans; Hepatocyte Nuclear Factor 1-beta; GRIK3; Gene Editing; 0303 health sciences; Cell Differentiation; Organoids; Kidney Tubules; CRISPR; glutamate receptors; Mutation; kidney RNA-seq; pluripotent stem cells; CRISPR-Cas Systems

Hepatocyte nuclear factor 1B (HNF1B) encodes a transcription factor expressed in developing human kidney epithelia. Heterozygous HNF1B mutations are the commonest monogenic cause of dysplastic kidney malformations (DKMs). To understand their pathobiology, we generated heterozygous HNF1B mutant kidney organoids from CRISPR-Cas9 gene-edited human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) reprogrammed from a family with HNF1B-associated DKMs. Mutant organoids contained enlarged malformed tubules displaying deregulated cell turnover. Numerous genes implicated in Mendelian kidney tubulopathies were downregulated, and mutant tubules resisted the cyclic AMP (cAMP)-mediated dilatation seen in controls. Bulk and single-cell RNA sequencing (scRNA-seq) analyses indicated abnormal Wingless/Integrated (WNT), calcium, and glutamatergic pathways, the latter hitherto unstudied in developing kidneys. Glutamate ionotropic receptor kainate type subunit 3 (GRIK3) was upregulated in malformed mutant nephron tubules and prominent in HNF1B mutant fetal human dysplastic kidney epithelia. These results reveal morphological, molecular, and physiological roles for HNF1B in human kidney tubule differentiation and morphogenesis illuminating the developmental origin of mutant-HNF1B-causing kidney disease.